scPDB - 4ez6 entry

Protein Data Bank Entry:

PDB ID : 4ez6

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2012-05-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA polymerase I
ID:	Q5KWC1_GEOKA
AC:	Q5KWC1
Organism:	Geobacillus kaustophilus
Reign:	Bacteria
TaxID:	235909
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	32.825
Number of residues:	23
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.077	1032.750

% Hydrophobic	% Polar
28.43	71.57
According to VolSite

Ligand :

HET Code:	DG3
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	-
Buried Surface Area:	40.84 %
Polar Surface area:	295.1 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
128.361	-25.0592	42.718

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O2B	OG	SER- 655	3.34	156.06	H-Bond (Protein Donor)	false
O1B	NE2	GLN- 656	3.44	139.85	H-Bond (Protein Donor)	false
O1A	N	GLN- 656	3.13	154.17	H-Bond (Protein Donor)	false
N1	OE1	GLU- 658	3.02	153.54	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 658	3.19	141.23	H-Bond (Ligand Donor)	false
O1G	NH2	ARG- 702	3.35	126.47	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 702	2.7	153.05	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 702	2.64	133.81	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 702	3.44	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 702	3.8	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 706	2.93	156.85	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 706	3.43	126.29	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 706	2.93	0	Ionic (Protein Cationic)	false
C1'	CB	LYS- 706	4.44	0	Hydrophobic	false
C4'	CD	LYS- 706	3.96	0	Hydrophobic	false
C1'	CD2	TYR- 710	4.26	0	Hydrophobic	false
C5'	CE2	TYR- 710	3.88	0	Hydrophobic	false
O6	O	HOH- 1030	2.67	179.95	H-Bond (Protein Donor)	false
O1A	O	HOH- 1131	2.91	162.48	H-Bond (Protein Donor)	false